ArticleFrontiers in genetics2012
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science.
Article in Frontiers in genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 2 of them syntheses that pooled it.
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Who cites it
49 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Data integration through proximity-based networks provides biological principles of organization across scales.The Plant cell · 2013Pooled it
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- New Insights on the Role of ß-Cyanoalanine Synthase CAS-C1 in Root Hair Elongation through Single-Cell Proteomics.Plants (Basel, Switzerland) · 2023Article
- Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation.Antioxidants (Basel, Switzerland) · 2023Article
- Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions.Frontiers in plant science · 2023Article
- Identification of Differentially Expressed Genes in Resistant Tetraploid Wheat (International journal of molecular sciences · 2022Article
- Micro-RNA-RegulatedPlants (Basel, Switzerland) · 2022Article
- PlantGSAD: a comprehensive gene set annotation database for plant species.Nucleic acids research · 2022Article
- Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote).Annals of botany · 2021Article
- Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date.BMC genomics · 2021Article
- Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of HAntioxidants (Basel, Switzerland) · 2021Article
- Article
- RNA Sequencing Analyses for Deciphering Potato Molecular Responses.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Abscisic Acid-Triggered Persulfidation of the Cys Protease ATG4 Mediates Regulation of Autophagy by Sulfide.The Plant cell · 2020Article
- Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives.International journal of molecular sciences · 2020Review
- Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis.Scientific reports · 2020Article
- Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds.Journal of experimental botany · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since the introduction of the Gene Ontology (GO), the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis) with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of co-expression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies.
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